[2023-06-05 18:40:28,397] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:40:28,399] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:40:28,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference
[2023-06-05 18:40:29,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:40:29,536] [INFO] Task started: Prodigal
[2023-06-05 18:40:29,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg520dbbc6-a2a9-405c-8886-f2bf51c92b71/GCA_902836875.1_MGYG-HGUT-04886_genomic.fna.gz | prodigal -d GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/cds.fna -a GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:40:32,845] [INFO] Task succeeded: Prodigal
[2023-06-05 18:40:32,845] [INFO] Task started: HMMsearch
[2023-06-05 18:40:32,845] [INFO] Running command: hmmsearch --tblout GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/reference_markers.hmm GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:40:33,008] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:40:33,009] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg520dbbc6-a2a9-405c-8886-f2bf51c92b71/GCA_902836875.1_MGYG-HGUT-04886_genomic.fna.gz]
[2023-06-05 18:40:33,027] [INFO] Query marker FASTA was written to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/markers.fasta
[2023-06-05 18:40:33,027] [INFO] Task started: Blastn
[2023-06-05 18:40:33,027] [INFO] Running command: blastn -query GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/reference_markers.fasta -out GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:40:33,577] [INFO] Task succeeded: Blastn
[2023-06-05 18:40:33,581] [INFO] Selected 20 target genomes.
[2023-06-05 18:40:33,581] [INFO] Target genome list was writen to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/target_genomes.txt
[2023-06-05 18:40:33,586] [INFO] Task started: fastANI
[2023-06-05 18:40:33,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg520dbbc6-a2a9-405c-8886-f2bf51c92b71/GCA_902836875.1_MGYG-HGUT-04886_genomic.fna.gz --refList GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/target_genomes.txt --output GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:40:45,058] [INFO] Task succeeded: fastANI
[2023-06-05 18:40:45,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:40:45,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:40:45,061] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:40:45,061] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:40:45,061] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-05 18:40:45,063] [INFO] DFAST Taxonomy check result was written to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/tc_result.tsv
[2023-06-05 18:40:45,063] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:40:45,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:40:45,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/checkm_data
[2023-06-05 18:40:45,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:40:45,108] [INFO] Task started: CheckM
[2023-06-05 18:40:45,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/checkm_input GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/checkm_result
[2023-06-05 18:41:02,836] [INFO] Task succeeded: CheckM
[2023-06-05 18:41:02,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:41:02,901] [INFO] ===== Completeness check finished =====
[2023-06-05 18:41:02,901] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:41:02,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/markers.fasta)
[2023-06-05 18:41:02,903] [INFO] Task started: Blastn
[2023-06-05 18:41:02,903] [INFO] Running command: blastn -query GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ca71c7-7625-47bb-b884-3979f2843a6f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:41:03,959] [INFO] Task succeeded: Blastn
[2023-06-05 18:41:03,963] [INFO] Selected 13 target genomes.
[2023-06-05 18:41:03,963] [INFO] Target genome list was writen to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:41:03,965] [INFO] Task started: fastANI
[2023-06-05 18:41:03,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg520dbbc6-a2a9-405c-8886-f2bf51c92b71/GCA_902836875.1_MGYG-HGUT-04886_genomic.fna.gz --refList GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/target_genomes_gtdb.txt --output GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:41:08,704] [INFO] Task succeeded: fastANI
[2023-06-05 18:41:08,713] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:41:08,713] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_900549635.1	s__CAG-170 sp900549635	95.0968	299	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.02	95.99	0.80	0.73	4	conclusive
GCA_003516765.1	s__CAG-170 sp003516765	85.335	224	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	96.93	96.75	0.73	0.72	5	-
GCA_002437575.1	s__CAG-170 sp002437575	82.8115	232	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432135.1	s__CAG-170 sp000432135	80.9122	143	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.47	98.15	0.85	0.82	4	-
GCA_002404795.1	s__CAG-170 sp002404795	79.656	137	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	-
GCA_000436735.1	s__CAG-170 sp000436735	79.5417	136	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.61	96.80	0.78	0.67	4	-
GCA_004555655.1	s__CAG-170 sp004555655	78.7505	124	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553545.1	s__CAG-170 sp900553545	78.5474	106	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.26	97.22	0.73	0.69	3	-
GCA_016297855.1	s__CAG-170 sp016297855	78.4538	85	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214155.1	s__CAG-170 sp905214155	78.0243	118	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803075.1	s__CAG-170 sp902803075	77.5815	81	388	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:41:08,717] [INFO] GTDB search result was written to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/result_gtdb.tsv
[2023-06-05 18:41:08,717] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:41:08,720] [INFO] DFAST_QC result json was written to GCA_902836875.1_MGYG-HGUT-04886_genomic.fna/dqc_result.json
[2023-06-05 18:41:08,720] [INFO] DFAST_QC completed!
[2023-06-05 18:41:08,720] [INFO] Total running time: 0h0m40s